The personal blog of Dave Fernig, thoughts on science and unrelated matters

Archive for November, 2012

A recent post on Retraction Watch is a reminder to all what it really means to be a scientist, researcher and teacher.

Dr. Pavičić from the University of Zagreb has retracted a paper in Physical Review Letters after a fatal error, which escaped him and all those who scrutinised the manuscript, was brought to his attention by a student. Dr. Pavičić went on to congratulate the student for his/her insight and to write a paper (on arXiv) explaining the errors.

Dr. Pavičić’s manner of dealing with the error is perhaps regarded as exemplary, but really should be regarded as “normal” for a scientist, researcher and teacher. Sadly, in the current climate many may find his exemplary behaviour unusual. He is certainly worthy of our collective congratulations for remaining true to science.

Raphael’s paper in Small on the likeliness (or lack of) of ligands self-assembling into stripes on nanoparticles is finally published. As Raphael notes, this took three years (plus six months at journals that would not touch the paper). Hats off to Small for letting science work as it should, that is through debate.

However, the process is slooooow. Why? Simply because we no longer operate in the agora where everyone meets regularly. Consequently, it is possible for substantial delay to occur whilst editors request a right of reply, something over which journal editors have no control. As Raphael’s Head of Department, I would say that this makes the process quite destructive with respect to the career of young tenure track staff who need to get papers out just to stay in the system. So, as ever, the established have a lever over the unestablished.

So how does a Head of Department judge such a polemic and come to a decision that has to be defended in discussions with senior management, when we justify budgets, hirings, tenure decisions and so on? My initial approach was to discuss some of the underlying techniques, such as scanning probe microscopy, with which I am familiar, with leading technical experts outside my own institution and the nanoparticle field. This allowed me to appreciate the limits of measurement and so come to an independent view. The upshot is I defended Raphael’s position and now senior management appreciate the importance of Raphael’s contribution to scientific debate.

Where now? Polemic aside, what I would like to see is experts in the measurements, who will not be in the nanoparticle field, to weigh in with their views and, importantly, advice. In this way the community will gain with respect to making technically challenging measurements, be it by scanning probe microscopy, spectroscopy or some other technique. We might then be able to make some progress.

Finally, one should always remember that science is a series of progressive approximations. Newton is “wrong”, but works fine to get you to Mars and back. I don’t think this has been put better than by Richard Feynman in his 1964 lecture from which we have this excerpt, entitled “The Key to Science“.

Dr Guerrini’s work, stretching over 25 years, has been concerned with investigating structure and function relationships in glycosaminoglycans. There are a biologically important family of structurally complex polysaccharides, which lie at the heart of many intercellular signalling processes, including those targeted in regenerative medicine and those disrupted in major diseases such as cancers and inflammatory conditions. His work also underpins our understanding of one of the lynchpins of modern medicine, the anticoagulant heparin. Highlights of Marco’s work have included the identification (in 2007-8) of toxic contaminants in pharmaceutical heparin, which had escaped the notice of regulatory authorities and lead to many deaths, and evidence exploding the myth of exquisite specificity in heparin-antithrombin interactions. Dr Guerrini ‘s talk will provide an introduction to this important class of polysaccharides, the principle methods that he uses currently, which are mainly NMR-based, but augmented by other complementary techniques, and will describe detailed structural studies of several interactions in solution. The talk will offer a rare opportunity to hear about interaction studies largely from the perspective of the saccharide ligand, which is often neglected, and will describe approaches that are highly complementary to the structural, functional and systems level studies currently being undertaken in IIB.

Professor Alan Waggoner, Director, Molecular Biosensor and Imaging Center, Carnegie Mellon University
will deliver the autumn Leica seminar on Wednesday 14th November at 5pm
Lecture Theatre 3, Life Sciences Building, with a post lecture reception at 6.15pm in the foyer outside the lecture theatre.

The lecture is free, but if you wish to attend can you let Kate Goodheart (kategf@liverpool.ac.uk) know for catering purposes.

Background information
Dr. Waggoner’s research group creates fluorescence-based detection systems for biology and biotechnology. The cyanine dye fluorescent labelling reagents developed in the laboratory have become widely used in industry and academic research for multicolour analysis of proteins, nucleic acids, cells and tissues by imaging and flow cytometry. The laboratory has participated in a wide range of research projects. As part of a NASA funded project his group produced a panel of fluorescent reagents and an imaging system, which detected sparse microbial life in the extreme environment of the Atacama desert. They are also developing new fluorescent reagents to monitor cellular electrical potential and ion fluxes to study the cardiac function of living mammalian hearts.
Dr. Waggoner is currently leading the Molecular Biosensor and Imaging Center into creating a novel sensor unit technology for a broad class of biosensors. He envisions this technology will provide a very powerful, and almost generic, tool for detecting protein interactions on and inside living cells. The sensor units are generated by combining engineered, cell-expressed target-binding proteins and environmentally sensitive fluorescent dyes that report target binding. Multiple sensors can be expressed simultaneously to sensitively and rapidly detect several targets within individual cells.
These sensor units are being incorporated into intracellular sensors, sensor particles and optical fibre sensors for interstitial spaces in tissues, sensors on chips for in vitro assays, and sensors for high throughput automated homogeneous assays in pharmaceutical drug discovery.